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ViVan specifications

Information


Unique identifier OMICS_25975
Name ViVan
Alternative name Viral Variance Analysis
Interface Web user interface
Restrictions to use None
Input data A sample file, a reference file and a features file.
Input format FASTQ,GZIP+FASTA
Programming languages Python
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Noam Shomron

Information


Unique identifier OMICS_25975
Name ViVan
Alternative name Viral Variance Analysis
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Stability Stable
Maintained Yes

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Versioning


No version available

Maintainer


  • person_outline Noam Shomron

Publication for Viral Variance Analysis

ViVan citations

 (6)
library_books

Influenza A virus hemagglutinin glycosylation compensates for antibody escape fitness costs

2018
PLoS Pathog
PMCID: 5773227
PMID: 29346435
DOI: 10.1371/journal.ppat.1006796

[…] nstructed using the Nextera XT DNA Library Prep Kit (Illumina) and sequenced on the Illumina MiSeq platform according the manufacturer’s protocols. Variants for each library were then called with the ViVan pipeline[]. Variant frequencies were then compared between primer ID and ViVan calls which passed filter. […]

call_split

Increasing Clinical Severity during a Dengue Virus Type 3 Cuban Epidemic: Deep Sequencing of Evolving Viral Populations

2016
J Virol
PMCID: 4836355
PMID: 26889031
DOI: 10.1128/JVI.02647-15
call_split See protocol

[…] ble of producing enough sequencing data to enable identification of rare variants present in as low as a 1:1,000 ratio in samples of modest reference size. Improvements in accuracy were made with the ViVAN (Viral Variant ANalysis) pipeline (), a robust algorithm based on each variant allele's initial rate and read qualities, to differentiate between sequencing errors and actual population variants […]

call_split

Whole Genome Sequencing Analysis from the Chikungunya Virus Caribbean Outbreak Reveals Novel Evolutionary Genomic Elements

2016
PLoS Negl Trop Dis
PMCID: 4726740
PMID: 26807575
DOI: 10.1371/journal.pntd.0004402
call_split See protocol

[…] y-Nagel), quantified by picogreen, and fragmented as described previously []. Sequences were obtained with an Illumina NextSeq500 machine and aligned against the CNR20235 reference sequence using the ViVAn pipeline [], which differentiates statistically significant variants from total SNPs identified within reads. For example, patient 1, amplicon 1 presented 2557 SNPs in the quality filtered reads […]

library_books

Biogenesis, Function, and Applications of Virus Derived Small RNAs in Plants

2015
Front Microbiol
PMCID: 4637412
PMID: 26617580
DOI: 10.3389/fmicb.2015.01237

[…] 0 (). Notably, although vsiRNAs-based NGS technology is a more effective way to study virus ecology and populations, there is relatively high error rate. Thus, several computational pipelines such as ViVan (), ViVaMBC (), and LayerCake (), tools with different applications for analyzing viral deep sequencing data, have been developed.In summary, much of what we know already and what we will uncove […]

call_split

Viral Polymerase Helicase Complexes Regulate Replication Fidelity To Overcome Intracellular Nucleotide Depletion

2015
J Virol
PMCID: 4645662
PMID: 26311883
DOI: 10.1128/JVI.01553-15
call_split See protocol

[…] ils toolkit (http://code.google.com/p/ea-utils). The alignment step is performed using the Burrows-Wheeler Aligner (), and Pileup analysis is performed using SAMtools (). Once the pileup is done, the ViVAn bioinformatics pipeline was used to collect the data per position and calculate the variance at each nucleotide position by root mean square deviation (). These values were then used to determin […]

call_split

Group Selection and Contribution of Minority Variants during Virus Adaptation Determines Virus Fitness and Phenotype

2015
PLoS Pathog
PMCID: 4420505
PMID: 25941809
DOI: 10.1371/journal.ppat.1004838
call_split See protocol

[…] nce with a maximum 2 mismatches per read, and no gaps, using BWA v0.5.9. Alignments were processed using SAMTools to obtain a pileup of the called bases at each position. An in-house pipeline, termed ViVAN (Viral Variant ANalysis) [] was used to identify statistically significant variants above the background noise due to sequencing error, in every sufficiently covered site (>100x). Briefly, for e […]

Citations

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ViVan institution(s)
Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Institut Pasteur, Viral Populations and Pathogenesis, CNRS URA 3015, Paris, France; Department of Statistics and Operations Research, Tel Aviv University, Tel Aviv, Israel
ViVan funding source(s)
Supported in part by a fellowship from the Edmond J. Safra Center for Bioinformatics at Tel-Aviv University, by a grant from the France-Israel High Council for Research Scientific and Technological Cooperation and from the European Union Seventh Framework Programme [FP7/2007- 2013] under Grant Agreement n278433-PREDEMICS, in part by the ERC Starting [242719], the ANR-09-JCJC-0118 and in part by the Colton Family Foundation.

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